The rule in question (3500 calories deficit results in one pound of weight loss) is mostly true, even if oversimplified. The fact that your metabolism drops as your weight drops just means that the calorie/day input needs to drop correspondingly to maintain the same deficit.
As the article states, the fact that the weight loss isn't entirely fat is a minor error. Thus, the 3500 calorie guideline is maintained, as long as you remember that it is a deficit and not a static amount.